Population genetic portrait of Pakistani Lahore-Christians based on 32 STR loci

Aqsa Rubab,Fatima Tuz Zahra,Samia Saleem,Muhammad Shafique,Dennis Mcnevin,Ahmad Ali Shahid,Faqeeha Javed

doi:10.1038/s41598-020-76016-2

Abstract

Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFℓSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. A total of 147 alleles were observed in 15 loci and allele 11 at the TPOX locus was the most frequent with frequency value (0.464). The data revealed that the Christian population has unique genetic characteristics with respect to a few unusual alleles and their frequencies relative to the other Pakistani population. Significant deviations from Hardy–Weinberg equilibrium were found at two loci (D13S317, D18S51) after Boneferroni’s correction (p ≤ 0.003). The combined power of discrimination, combined power of exclusion and cumulative probability of matching were 0.999999999999999978430815060354, 0.999995039393942 and 2.15692 × 10−17, respectively. On the bases of genetic distances, PCA, phylogenetic and structure analysis Lahore-Christians appeared genetically more associated to south Asian particularly Indian populations like Tamil, Karnataka, Kerala and Andhra Pradesh than rest of global populations.

Highlights

Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFlSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples
Lahore-Christian samples were evaluated based on fifteen autosomal STRs of Identifiler Plus Kit (Applied Biosystems) and already published data set of same male samples (YA004381)[9] on 17 YSTRs (DYS438, DYS393, DYS385a⁄b, DYS389I⁄II, DYS458, DYS437, DYS391, DYS392, DYS635 (Y-GATA-C4), Y-GATA-H4, DYS19, DYS390, DYS439, DYS456, DYS448)
While we may have expected Christians to exhibit some differentiation from the other Pakistani populations, it is not surprising that Lahore-Christians and South Asian Tamil are not differentiated by the STRs in the Identifiler panel using Structure

Summary

Introduction

Phylogenetic relationship and the population structure of 500 individuals from the Christian community of Lahore, Pakistan, were examined based on 15 autosomal short tandem repeats (STRs) using the AmpFlSTR Identifiler Plus PCR Amplification Kit and our previously published Y-filer kit data (17 Y-STRs) of same samples. There have been many earlier studies of 15 autosomal STRs in various Pakistani populations except Christians. Lahore-Christian samples were evaluated based on fifteen autosomal STRs of Identifiler Plus Kit (Applied Biosystems) and already published data set of same male samples (YA004381)[9] on 17 YSTRs (DYS438, DYS393, DYS385a⁄b, DYS389I⁄II, DYS458, DYS437, DYS391, DYS392, DYS635 (Y-GATA-C4), Y-GATA-H4, DYS19, DYS390, DYS439, DYS456, DYS448). The allele frequencies at the autosomal STRs in the Lahore-Christian population were compared with those from other populations using population differentiation test as shown in Supplementary Table 4.

Results

Conclusion